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src/c/o/cogent-1.5.3/cogent/maths/stats/distribution.py   cogent(Download)
"""
from __future__ import division
from cogent.maths.stats.special import erf, erfc, igamc, igam, betai, log1p, \
    expm1, SQRTH, MACHEP, MAXNUM, PI, ndtri, incbi, igami, fix_rounding_error,\
    ln_binomial
    See Cephes docs for details.
    """
    x = fix_rounding_error(x)
    if x < 0:
        raise ValueError, "chi_low: x must be >= 0 (got %s)." % x
    See Cephes docs for details.
    """
    x = fix_rounding_error(x)
 
    if x < 0:
    See Cephes docs for details.
    """
    p = fix_rounding_error(p)
    if (p < 0) or (p > 1):
        raise ValueError, "Binomial p must be between 0 and 1."
    See Cephes docs for details.
    """
    p = fix_rounding_error(p)
    if (p < 0) or (p > 1):
        raise ValueError, "Binomial p must be between 0 and 1."

src/p/y/pycogent-HEAD/cogent/maths/stats/distribution.py   pycogent(Download)
"""
from __future__ import division
from cogent.maths.stats.special import erf, erfc, igamc, igam, betai, log1p, \
    expm1, SQRTH, MACHEP, MAXNUM, PI, ndtri, incbi, igami, fix_rounding_error,\
    ln_binomial
    See Cephes docs for details.
    """
    x = fix_rounding_error(x)
    if x < 0:
        raise ValueError, "chi_low: x must be >= 0 (got %s)." % x
    See Cephes docs for details.
    """
    x = fix_rounding_error(x)
 
    if x < 0:
    See Cephes docs for details.
    """
    p = fix_rounding_error(p)
    if (p < 0) or (p > 1):
        raise ValueError, "Binomial p must be between 0 and 1."
    See Cephes docs for details.
    """
    p = fix_rounding_error(p)
    if (p < 0) or (p > 1):
        raise ValueError, "Binomial p must be between 0 and 1."

src/c/o/cogent-1.5.3/cogent/format/mage.py   cogent(Download)
from cogent.util.misc import extract_delimited
from cogent.maths.stats.util import Freqs
from cogent.maths.stats.special import fix_rounding_error
 
__author__ = "Rob Knight"
        """
        # all values have to be between 0 and 1
        a = fix_rounding_error(self.X)
        c = fix_rounding_error(self.Y)
        g = fix_rounding_error(self.Z)
        #u = fix_rounding_error(1-a-c-g)
        if is_essentially(1, a+c+g, round_error=round_error):
            u = 0.0
        else:
            u = fix_rounding_error(1-a-c-g)

src/p/y/pycogent-HEAD/cogent/format/mage.py   pycogent(Download)
from cogent.util.misc import extract_delimited
from cogent.maths.stats.util import Freqs
from cogent.maths.stats.special import fix_rounding_error
 
__author__ = "Rob Knight"
        """
        # all values have to be between 0 and 1
        a = fix_rounding_error(self.X)
        c = fix_rounding_error(self.Y)
        g = fix_rounding_error(self.Z)
        #u = fix_rounding_error(1-a-c-g)
        if is_essentially(1, a+c+g, round_error=round_error):
            u = 0.0
        else:
            u = fix_rounding_error(1-a-c-g)

src/c/o/cogent-1.5.3/cogent/struct/dihedral.py   cogent(Download)
from numpy import array, cross, pi, cos, arccos as acos
from cogent.util.array import norm
from cogent.maths.stats.special import fix_rounding_error
 
class DihedralGeometryError(Exception): pass
        "Cannot calculate angle for vectors with length zero")
    cosine = scalar(v1,v2)/length_product
    angle = acos(fix_rounding_error(cosine))
    return angle
 

src/c/o/cogent-1.5.3/cogent/core/usage.py   cogent(Download)
from __future__ import division
from cogent.maths.stats.util import Freqs, Numbers, UnsafeFreqs
from cogent.maths.stats.special import fix_rounding_error
from cogent.util.array import euclidean_distance
from cogent.util.misc import Delegator, FunctionWrapper, InverseDict
        result = cls()
        x,y,z = coords
        u = fix_rounding_error((1-x-y-z)/-2)
        a, c, g = z-u, x-u, y-u
        result['A'] = a

src/p/y/pycogent-HEAD/cogent/struct/dihedral.py   pycogent(Download)
from numpy import array, cross, pi, cos, arccos as acos
from cogent.util.array import norm
from cogent.maths.stats.special import fix_rounding_error
 
class DihedralGeometryError(Exception): pass
        "Cannot calculate angle for vectors with length zero")
    cosine = scalar(v1,v2)/length_product
    angle = acos(fix_rounding_error(cosine))
    return angle
 

src/p/y/pycogent-HEAD/cogent/core/usage.py   pycogent(Download)
from __future__ import division
from cogent.maths.stats.util import Freqs, Numbers, UnsafeFreqs
from cogent.maths.stats.special import fix_rounding_error
from cogent.util.array import euclidean_distance
from cogent.util.misc import Delegator, FunctionWrapper, InverseDict
        result = cls()
        x,y,z = coords
        u = fix_rounding_error((1-x-y-z)/-2)
        a, c, g = z-u, x-u, y-u
        result['A'] = a